X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=387bba6c930e27a878c87e03c41649da31f7e696;hb=362bd0a813f302f28631d9c9447dd8aa9ee0ceda;hp=083a6b1bd6eb532cfd566ef1974a5e0367d92d3c;hpb=bb78bbf463fdbb67cfa123c94ddaa1e8f1d3c356;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 083a6b1..387bba6 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -21,15 +21,19 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; import java.awt.Font; -import org.forester.phylogeny.data.NodeVisualization; -import org.forester.phylogeny.data.NodeVisualization.NodeFill; -import org.forester.phylogeny.data.NodeVisualization.NodeShape; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; +import org.forester.phylogeny.data.NodeData; +import org.forester.phylogeny.data.NodeData.NODE_DATA; +import org.forester.phylogeny.data.NodeVisualData; +import org.forester.phylogeny.data.NodeVisualData.NodeFill; +import org.forester.phylogeny.data.NodeVisualData.NodeShape; import org.forester.util.ForesterUtil; /* @@ -37,49 +41,100 @@ import org.forester.util.ForesterUtil; */ final public class Options { - static final double MIN_CONFIDENCE_DEFAULT = 0.0; - private boolean _show_branch_length_values; - private boolean _internal_number_are_confidence_for_nh_parsing; - private boolean _show_scale; - private boolean _show_overview; - private boolean _antialias_screen; - private boolean _antialias_print; - private boolean _graphics_export_visible_only; - private int _print_size_x; - private int _print_size_y; - private double _min_confidence_value; - private boolean _print_black_and_white; - private boolean _print_using_actual_size; - private boolean _graphics_export_using_actual_size; - private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type; - private CLADOGRAM_TYPE _cladogram_type; - private OVERVIEW_PLACEMENT_TYPE _ov_placement; - private NODE_LABEL_DIRECTION _node_label_direction; - private Font _base_font; - private boolean _match_whole_terms_only; - private boolean _search_case_sensitive; - private float _print_line_width; - private boolean _inverse_search_result; - private double _scale_bar_length; - private short _number_of_digits_after_comma_for_confidence_values; - private short _number_of_digits_after_comma_for_branch_length_values; - private boolean _nh_parsing_replace_underscores; - private boolean _nh_parsing_extract_pfam_taxonomy_codes; - private boolean _editable; - private boolean _background_color_gradient; - private boolean _show_domain_labels; - private boolean _color_labels_same_as_parent_branch; - private boolean _abbreviate_scientific_names; - private NodeVisualization.NodeShape _default_node_shape; - private NodeVisualization.NodeFill _default_node_fill; - private short _default_node_shape_size; - private boolean _taxonomy_colorize_node_shapes; - private boolean _show_default_node_shapes; + static final double MIN_CONFIDENCE_DEFAULT = 0.0; + private boolean _abbreviate_scientific_names; + private boolean _allow_errors_in_distance_to_parent; + private boolean _antialias_print; + private boolean _antialias_screen; + private boolean _background_color_gradient; + private Font _base_font; + private CLADOGRAM_TYPE _cladogram_type; + private boolean _color_by_taxonomic_group; + private boolean _color_labels_same_as_parent_branch; + private NodeVisualData.NodeFill _default_node_fill; + private NodeVisualData.NodeShape _default_node_shape; + private short _default_node_shape_size; + private boolean _editable; + private NODE_DATA _ext_desc_data_to_return; + private boolean _graphics_export_using_actual_size; + private boolean _graphics_export_visible_only; + private boolean _internal_number_are_confidence_for_nh_parsing; + private boolean _inverse_search_result; + private boolean _match_whole_terms_only; + private double _min_confidence_value; + private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style; + private boolean _nh_parsing_replace_underscores; + private NODE_LABEL_DIRECTION _node_label_direction; + private short _number_of_digits_after_comma_for_branch_length_values; + private short _number_of_digits_after_comma_for_confidence_values; + private OVERVIEW_PLACEMENT_TYPE _ov_placement; + private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type; + private boolean _print_black_and_white; + private float _print_line_width; + private int _print_size_x; + private int _print_size_y; + private boolean _print_using_actual_size; + private double _scale_bar_length; + private boolean _search_case_sensitive; + private boolean _show_annotation_ref_source; + private boolean _show_confidence_stddev; + private boolean _show_default_node_shapes_external; + private boolean _show_default_node_shapes_internal; + private boolean _show_domain_labels; + private boolean _show_overview; + private boolean _show_scale; + private TAXONOMY_EXTRACTION _taxonomy_extraction; + private boolean _line_up_renderable_node_data; + private boolean _right_align_domains; private Options() { init(); } + public NodeData.NODE_DATA getExtDescNodeDataToReturn() { + return _ext_desc_data_to_return; + } + + public boolean isAllowErrorsInDistanceToParent() { + return _allow_errors_in_distance_to_parent; + } + + public boolean isAllowFontSizeChange() { + return true; + } + + public final boolean isShowAnnotationRefSource() { + return _show_annotation_ref_source; + } + + public final boolean isShowDomainLabels() { + return _show_domain_labels; + } + + public final void setAllowErrorsInDistanceToParent( final boolean allow_errors_in_distance_to_parent ) { + _allow_errors_in_distance_to_parent = allow_errors_in_distance_to_parent; + } + + public void setBackgroundColorGradient( final boolean background_color_gradient ) { + _background_color_gradient = background_color_gradient; + } + + public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { + _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; + } + + public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) { + _ext_desc_data_to_return = ext_desc_data_to_return; + } + + public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) { + _show_annotation_ref_source = show_annotation_ref_source; + } + + public void setShowDomainLabels( final boolean show_domain_labels ) { + _show_domain_labels = show_domain_labels; + } + final Font getBaseFont() { return _base_font; } @@ -104,6 +159,10 @@ final public class Options { return _min_confidence_value; } + NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportValueStyle() { + return _nh_conversion_support_value_style; + } + final NODE_LABEL_DIRECTION getNodeLabelDirection() { return _node_label_direction; } @@ -140,50 +199,8 @@ final public class Options { return _scale_bar_length; } - final private void init() { - _default_node_shape = NodeShape.CIRCLE; - _default_node_fill = NodeFill.GRADIENT; - _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; - _taxonomy_colorize_node_shapes = false; - _show_branch_length_values = false; - _internal_number_are_confidence_for_nh_parsing = false; - _show_scale = false; - _antialias_screen = true; - _antialias_print = true; - _graphics_export_visible_only = false; - _editable = true; - _background_color_gradient = false; - _show_default_node_shapes = false; - if ( Util.isUsOrCanada() ) { - _print_size_x = Constants.US_LETTER_SIZE_X; - _print_size_y = Constants.US_LETTER_SIZE_Y; - } - else { - _print_size_x = Constants.A4_SIZE_X; - _print_size_y = Constants.A4_SIZE_Y; - } - _min_confidence_value = MIN_CONFIDENCE_DEFAULT; - _print_black_and_white = false; - _print_using_actual_size = false; - _graphics_export_using_actual_size = true; - _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; - _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 ); - _match_whole_terms_only = false; - _search_case_sensitive = false; - _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; - _show_overview = true; - _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT; - _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL; - _inverse_search_result = false; - _scale_bar_length = 0.0; - _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; - _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT; - _nh_parsing_replace_underscores = false; - _nh_parsing_extract_pfam_taxonomy_codes = false; - _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; - _show_domain_labels = true; - setAbbreviateScientificTaxonNames( false ); - _color_labels_same_as_parent_branch = false; + final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + return _taxonomy_extraction; } final boolean isAbbreviateScientificTaxonNames() { @@ -206,6 +223,10 @@ final public class Options { return _background_color_gradient; } + final boolean isColorByTaxonomicGroup() { + return _color_by_taxonomic_group; + } + final boolean isColorLabelsSameAsParentBranch() { return _color_labels_same_as_parent_branch; } @@ -214,10 +235,6 @@ final public class Options { return _editable; } - final boolean isExtractPfamTaxonomyCodesInNhParsing() { - return _nh_parsing_extract_pfam_taxonomy_codes; - } - final boolean isGraphicsExportUsingActualSize() { return _graphics_export_using_actual_size; } @@ -254,12 +271,16 @@ final public class Options { return _search_case_sensitive; } - final boolean isShowBranchLengthValues() { - return _show_branch_length_values; + boolean isShowConfidenceStddev() { + return _show_confidence_stddev; } - public final boolean isShowDomainLabels() { - return _show_domain_labels; + boolean isShowDefaultNodeShapesExternal() { + return _show_default_node_shapes_external; + } + + boolean isShowDefaultNodeShapesInternal() { + return _show_default_node_shapes_internal; } final boolean isShowOverview() { @@ -270,10 +291,6 @@ final public class Options { return _show_scale; } - boolean isTaxonomyColorizeNodeShapes() { - return _taxonomy_colorize_node_shapes; - } - final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { _abbreviate_scientific_names = abbreviate_scientific_names; } @@ -286,10 +303,6 @@ final public class Options { _antialias_screen = antialias_screen; } - public void setBackgroundColorGradient( final boolean background_color_gradient ) { - _background_color_gradient = background_color_gradient; - } - final void setBaseFont( final Font base_font ) { _base_font = base_font; } @@ -298,8 +311,8 @@ final public class Options { _cladogram_type = cladogram_type; } - public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { - _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; + final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) { + _color_by_taxonomic_group = color_by_taxonomic_group; } final void setDefaultNodeFill( final NodeFill default_node_fill ) { @@ -318,10 +331,6 @@ final public class Options { _editable = editable; } - final void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) { - _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes; - } - final void setGraphicsExportUsingActualSize( final boolean graphics_export_using_actual_size ) { _graphics_export_using_actual_size = graphics_export_using_actual_size; if ( !graphics_export_using_actual_size ) { @@ -352,16 +361,12 @@ final public class Options { _min_confidence_value = min_confidence_value; } - final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { - _node_label_direction = node_label_direction; + void setNhConversionSupportValueStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_value_style ) { + _nh_conversion_support_value_style = nh_conversion_support_value_style; } - final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) { - _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values; - } - - final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) { - _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values; + final void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { + _node_label_direction = node_label_direction; } final void setOvPlacement( final OVERVIEW_PLACEMENT_TYPE ov_placement ) { @@ -404,12 +409,16 @@ final public class Options { _search_case_sensitive = search_case_sensitive; } - final void setShowBranchLengthValues( final boolean show_branch_length_values ) { - _show_branch_length_values = show_branch_length_values; + void setShowConfidenceStddev( final boolean show_confidence_stddev ) { + _show_confidence_stddev = show_confidence_stddev; } - public void setShowDomainLabels( final boolean show_domain_labels ) { - _show_domain_labels = show_domain_labels; + void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) { + _show_default_node_shapes_external = show_default_node_shapes_external; + } + + void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { + _show_default_node_shapes_internal = show_default_node_shapes_internal; } final void setShowOverview( final boolean show_overview ) { @@ -420,20 +429,67 @@ final public class Options { _show_scale = show_scale; } - void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { - _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; + final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; } - final static Options createDefaultInstance() { - return new Options(); + final private void init() { + _default_node_shape = NodeShape.CIRCLE; + _default_node_fill = NodeFill.GRADIENT; + _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; + _internal_number_are_confidence_for_nh_parsing = false; + _show_scale = false; + _antialias_screen = true; + _antialias_print = true; + _graphics_export_visible_only = false; + _editable = true; + _background_color_gradient = false; + _show_default_node_shapes_internal = false; + _show_default_node_shapes_external = false; + if ( AptxUtil.isUsOrCanada() ) { + _print_size_x = Constants.US_LETTER_SIZE_X; + _print_size_y = Constants.US_LETTER_SIZE_Y; + } + else { + _print_size_x = Constants.A4_SIZE_X; + _print_size_y = Constants.A4_SIZE_Y; + } + _min_confidence_value = MIN_CONFIDENCE_DEFAULT; + _print_black_and_white = false; + _print_using_actual_size = true; + _graphics_export_using_actual_size = true; + _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; + _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 ); + _match_whole_terms_only = false; + _search_case_sensitive = false; + _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; + _show_overview = true; + _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT; + _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL; + _inverse_search_result = false; + _scale_bar_length = 0.0; + _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; + _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT; + _nh_parsing_replace_underscores = false; + _taxonomy_extraction = TAXONOMY_EXTRACTION.NO; + _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; + _show_domain_labels = true; + _show_annotation_ref_source = true; + setAbbreviateScientificTaxonNames( false ); + _color_labels_same_as_parent_branch = false; + _show_confidence_stddev = false; + _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE; + _ext_desc_data_to_return = NODE_DATA.UNKNOWN; + _line_up_renderable_node_data = true; + _right_align_domains = false; } - boolean isShowDefaultNodeShapes() { - return _show_default_node_shapes; + final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) { + _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values; } - void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) { - _show_default_node_shapes = show_default_node_shapes; + final private void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) { + _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values; } public final static Options createInstance( final Configuration configuration ) { @@ -441,8 +497,8 @@ final public class Options { if ( configuration != null ) { instance.setAntialiasScreen( configuration.isAntialiasScreen() ); instance.setShowScale( configuration.isShowScale() ); - instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() ); instance.setShowOverview( configuration.isShowOverview() ); + instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() ); instance.setCladogramType( configuration.getCladogramType() ); instance.setOvPlacement( configuration.getOvPlacement() ); instance.setPrintLineWidth( configuration.getPrintLineWidth() ); @@ -456,13 +512,14 @@ final public class Options { instance.setNumberOfDigitsAfterCommaForConfidenceValues( configuration .getNumberOfDigitsAfterCommaForConfidenceValues() ); } - instance.setExtractPfamTaxonomyCodesInNhParsing( configuration.isExtractPfamTaxonomyCodesInNhParsing() ); + instance.setTaxonomyExtraction( configuration.getTaxonomyExtraction() ); instance.setReplaceUnderscoresInNhParsing( configuration.isReplaceUnderscoresInNhParsing() ); instance.setInternalNumberAreConfidenceForNhParsing( configuration .isInternalNumberAreConfidenceForNhParsing() ); instance.setEditable( configuration.isEditable() ); instance.setColorLabelsSameAsParentBranch( configuration.isColorLabelsSameAsParentBranch() ); instance.setShowDomainLabels( configuration.isShowDomainLabels() ); + instance.setShowAnnotationRefSource( configuration.isShowAnnotationRefSource() ); instance.setAbbreviateScientificTaxonNames( configuration.isAbbreviateScientificTaxonNames() ); if ( configuration.getMinConfidenceValue() != MIN_CONFIDENCE_DEFAULT ) { instance.setMinConfidenceValue( configuration.getMinConfidenceValue() ); @@ -492,25 +549,39 @@ final public class Options { if ( configuration.getDefaultNodeShapeSize() >= 0 ) { instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() ); } - instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() ); - instance.setShowDefaultNodeShapes( configuration.isShowDefaultNodeShapes() ); + instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() ); + instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() ); + if ( configuration.getExtDescNodeDataToReturn() != null ) { + instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() ); + } + instance.setRightLineUpDomains( configuration.isRightLineUpDomains() ); + instance.setLineUpRendarableNodeData( configuration.isLineUpRendarableNodeData() ); + instance.setAllowErrorsInDistanceToParent( false ); } return instance; } - static enum CLADOGRAM_TYPE { - NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP; + final static Options createDefaultInstance() { + return new Options(); + } + + public static enum CLADOGRAM_TYPE { + EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP; } - static enum NODE_LABEL_DIRECTION { + public static enum NODE_LABEL_DIRECTION { HORIZONTAL, RADIAL; } + public static enum PHYLOGENY_GRAPHICS_TYPE { + CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED; + } + static enum OVERVIEW_PLACEMENT_TYPE { - UPPER_LEFT( "upper left" ), - UPPER_RIGHT( "upper right" ), LOWER_LEFT( "lower left" ), - LOWER_RIGHT( "lower right" ); + LOWER_RIGHT( "lower right" ), + UPPER_LEFT( "upper left" ), + UPPER_RIGHT( "upper right" ); private final String _name; @@ -528,7 +599,19 @@ final public class Options { } } - static enum PHYLOGENY_GRAPHICS_TYPE { - RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR; + final public boolean isLineUpRendarableNodeData() { + return _line_up_renderable_node_data; + } + + final public boolean isRightLineUpDomains() { + return _right_align_domains; + } + + final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) { + _line_up_renderable_node_data = line_up_renderable_node_data; + } + + final public void setRightLineUpDomains( final boolean right_align_domains ) { + _right_align_domains = right_align_domains; } }